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The new classification of
eukaryotes
Sina M. Adl
University of Saskatchewan
ISOP taxonomy and revisions,
what we learned during this process
1998
• 1980, Levine & 15 others, A newly revised classification
of the Protozoa. J. Protozoology 27:37-58.
• Protist class...
1998-2003
• 1998, ISOP was not interested, “too difficult”
• Mark Farmer’s attempt (~2000)
– Ranks were a problem
– No agr...
• 1999, the debacle of the Illustrated Guide 2nd edn
– Loss of civility and respectful behaviour
– Ego before science and ...
2002-2005
• Emergence of tree builders, who didn’t know
their groups
• Conversations on groups and phylogeny
impossible
– ...
Problems with traditional codes
• Based on Aristotle and Linnaeus
– Predate idea of “common decent” and
evolution (Darwin ...
Other issues
• ICBN species described
in Latin
• The Codes do not
accommodate each other
• Type-specimen rules
impractical...
Codes failed to provide name stability
• Electron microscopy & DNA sequence
information
– many changes to groups and names...
Towards a new system
• Provide some formality
• Designating group names, authority,
definitions
• Clades monophyletic (as ...
Solutions to consider
• Classification system must ensure species
name stability
– Genus epithet, genus.epithet, genus-epi...
Solutions to consider (next)
• Phonetic names with descriptions in
any language, translatable
• New rules for type specime...
Systematics
• Adopted a name-less rank system, with formal
definitions
– Polyphyletic groups indicated
– Retain older name...
PhyloCode
• A modern code
– Apomorphy
– Branch-based
– Node-based
– Groups related “by common descent”
• Corrects most pro...
2005
• 2004, ISOP interested in the manuscript
– An issue of J. Euk. Microbiol.
• 1 CD of emails over 3 years of
discussio...
Phylogeny vs classification
• Phylogeny guides classification
– Wrong end of the tree
– Common terms, informal names
• Del...
…but what are species?
• How much sequence divergence?
• How much biogeographical sampling?
• Identical morphology but dif...
Organiser, non-partisan, knows
the field and people well,
well-known, diplomat, arbitrator
Subject expert, respected,
work...
Work in progress…
• New rules for protist type specimen
– Digital web-based species data-base
• Your good ideas and discus...
International codes of nomenclature
• Rules of the system for classifying
and naming species
– Int. Code Botanical Nomen.
...
Definitions
• Systematics
– According to a system
• Taxonomy
– A system of classifying
• Classification
– Placing into cat...
The new classification of eukaryotes
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The new classification of eukaryotes

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Presented during the first EukRef workshop organized in Vancouver, Canada (July 2015).

Publié dans : Sciences
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The new classification of eukaryotes

  1. 1. The new classification of eukaryotes Sina M. Adl University of Saskatchewan
  2. 2. ISOP taxonomy and revisions, what we learned during this process
  3. 3. 1998 • 1980, Levine & 15 others, A newly revised classification of the Protozoa. J. Protozoology 27:37-58. • Protist classification pre-1997 • Glimmer of synthesis, 1998 • 1997, Yves van der Peer & Rupert de Wachter, J. Molec. Evol. 45:619-630 – Complete phylogenetic tree of eukaryotes • ISOP had not shown involvement or leadership – ISEP, IJSEM • Very exciting period, but loss of name stability • Protists disappeared from text books and courses
  4. 4. 1998-2003 • 1998, ISOP was not interested, “too difficult” • Mark Farmer’s attempt (~2000) – Ranks were a problem – No agreement on names – No agreement on lineages – More than ever before, zoological and botanical codes were intermingled (and some lineage names duplicated) – No co-operation – Couldn’t be assembled from the literature
  5. 5. • 1999, the debacle of the Illustrated Guide 2nd edn – Loss of civility and respectful behaviour – Ego before science and hypothesis testing • Insufficient data, personal classifications, grounded in imagination and possibilities • Obvious failure of the Codes (ICZN, ICBN) – No name stability – Independence of individuals to make things up – Incompatible codes
  6. 6. 2002-2005 • Emergence of tree builders, who didn’t know their groups • Conversations on groups and phylogeny impossible – Every lab its own vocabulary • Patiently, group by group, microscopists identified, lineages re-described, reassembled, names and authorities discussed – Hard part, how to assemble these groups – which rules to use?
  7. 7. Problems with traditional codes • Based on Aristotle and Linnaeus – Predate idea of “common decent” and evolution (Darwin 1859) – Believed in fixed number of species • Moving species changes its name • Rank change causes cascade of name changes • More emphasis on authority than name stability See Adl & 19 others, 2007, J. Systematic Biology 56
  8. 8. Other issues • ICBN species described in Latin • The Codes do not accommodate each other • Type-specimen rules impractical or useless for many protists
  9. 9. Codes failed to provide name stability • Electron microscopy & DNA sequence information – many changes to groups and names – multiple names created for the same groups – use of common terms, without specifying authority or definition or delineation • Loss of species name, when moved, is a bad system for filing and finding again
  10. 10. Towards a new system • Provide some formality • Designating group names, authority, definitions • Clades monophyletic (as possible) • Classification based on name-less ranks • Prevents name changes in higher ranks • Easier to revise Adl & 28 others, 2005, J.E.M. 52 (5).
  11. 11. Solutions to consider • Classification system must ensure species name stability – Genus epithet, genus.epithet, genus-epithet, genusepithet Adl & 19 others, 2007, Systematic Biology • Nested clades as PhyloCode – Separates naming clades from assembling hierarchy • To modernise or replace traditional codes – Rules should be few, simple, practical
  12. 12. Solutions to consider (next) • Phonetic names with descriptions in any language, translatable • New rules for type specimen – Digital images – DNA sequence – Biological information • Must be public, free, web-based
  13. 13. Systematics • Adopted a name-less rank system, with formal definitions – Polyphyletic groups indicated – Retain older names, emended – Eliminate empty ranks – Ignore rank endings as an accident of history – Allows groups to be moved and modified, without changing their names • Problems with using traditional codes summarised – Adl & 19 others, 2007, J. Systematic Biology 56
  14. 14. PhyloCode • A modern code – Apomorphy – Branch-based – Node-based – Groups related “by common descent” • Corrects most problems in ICBN & ICZN • Did not deal with naming species and type-specimen • Code is ready, not implemented Cantino & de Queiroz 2006, Phylocode
  15. 15. 2005 • 2004, ISOP interested in the manuscript – An issue of J. Euk. Microbiol. • 1 CD of emails over 3 years of discussions – 1 manuscript • To distinguish between phylogeny and classification – Separation of assembling nested hierarchies, from naming clades – Standardising names of clades – The return of name stability
  16. 16. Phylogeny vs classification • Phylogeny guides classification – Wrong end of the tree – Common terms, informal names • Delineation of groups missing, which genera are in, and which are excluded?
  17. 17. …but what are species? • How much sequence divergence? • How much biogeographical sampling? • Identical morphology but different species! • Selection acts on ecological parameters – 3D niche space must be part of the solution • Issues now facing environmental data
  18. 18. Organiser, non-partisan, knows the field and people well, well-known, diplomat, arbitrator Subject expert, respected, works well with people Basic modular structure Group or subject experts, detailed deep knowledge, diversified opinions External comments on outcome, discussions, revisions
  19. 19. Work in progress… • New rules for protist type specimen – Digital web-based species data-base • Your good ideas and discussions are welcome
  20. 20. International codes of nomenclature • Rules of the system for classifying and naming species – Int. Code Botanical Nomen. – Int. Code Zool. Nomen. – Int. Code Cultivated Plants – Int Code Microbiol. Nomen. – PhyloCode
  21. 21. Definitions • Systematics – According to a system • Taxonomy – A system of classifying • Classification – Placing into categories • eg. Species into named groups, by common descent • Nomenclature – A system (set of rules) of naming Source: Oxford dictionary of current English 3rd edn, 2001

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